The Troublesome Tales of Sherlock and Moriarty
by A-Glittering-Star-Night
Summary: A mysterious murder, A sad and lonely detective and one big secret behind it all. Friends are spilt, family divided. Nothing will be the same again. John thought science couldn't be that more strange. He thought wrong..
1. Chapter 1: The Narration of The Incident

**_The Troublesome Tale of Sherlock and Moriarty_**

Chapter 1: The Narration of the Incident

 _Prologue: John thought science couldn't get much more advanced. He thought wrong. Everything was about to get a whole lot strange. This was only the beginning of a wild and unpredictable experiment._

Chapter 1:

John and Mycroft were strolling merrily down the street after eating at their local fish and chip shop. Every Friday they ate fish and chips while catching up with each other. Now, they stopped at 221b Baker Street to discuss an important affair. One that was about to change their lives forever and they did not even realise it.

 **~OooO~**

"John, this catch up was adequate. Sherlock isn't that communicative these days." Mycroft said, thinking about his younger brother, Sherlock Holmes; the consulting detective, who had gone silent to the rest of the world.

"Sherlock has gone rather strange these days" John said, trying to remember Sherlock before he had locked himself away. Sherlock had gone to extreme measures to be alone.

"Yes, he has." Mycroft paused. "Another thing that has cropped up that is strange happened a few days ago"

"What happened?" John said.

"It was an appalling incident" Mycroft said, he quickly stopped looking at his umbrella and stared at John

"Really? I thought it wasn't that much of a big deal" John said, oblivious to Mycroft's concerned face.

"`Well." Mycroft paused "A strange man apparently trampled an innocent teenage girl."

"Really." John said, blown away by the odd news. "Shall we call him a villain or a criminal? It seems insulting to call a man we haven't even know properly 'strange' " John said strangely

"Criminal" Mycroft announced quickly, avoiding a quick glance at the door to Sherlock's house

"Okay criminal it is" John said, a bit too loudly, John quickly inspected the street, no one was near enough to hear him.

"The criminal hasn't been spotted before. He seems peculiar….. and diverse" Mycroft said, he looked immersed in thought.

"Diverse?" John asked still curious at this criminal of a man that Mycroft was talking about. John had not heard about this, why had this not been on the news? Was it that strange?

"The criminal seemed too grotesque than anyone else. I cannot put my finger on it. It feels strange, not knowing anything" Mycroft said looking pessimistic and forlorn.

"So can you tell me exactly what happened that night" John asked eagerly, he was craving for more knowledge on this event that got Mycroft bewildered and Mycroft never got bewildered.

"Well, it happened earlier this week. Monday to be exact." Mycroft said, telling John of the incident.

"A girl was walking home from a date with her boyfriend." Mycroft said, neglecting to see John's bemused facial expression.

"This seems very normal" John articulated. Mycroft glared at John, but he carried on regardless.

"Walking behind the girl was a man, he wore a long dark coat which concealed his disguised face."

"You have started to get my attention, carry on" John uttered

"The criminal pushed her over and kept on walking. Since the girl was just outside her house, her family found her quickly after she had to started to scream in pure agony." Mycroft said.

"What else?" John asked disappointedly, as he thought it would be more interesting than it seemed to be.

"That is all I have heard" Mycroft said, he seemed disturbed.

"Did they press charges? or anything?" John asked curious about the criminal, who John started to dislike.

"Allegedly, the family pressed charges against him. I believe it to be one hundred pounds. He paid after an hour of receiving the knowledge that he had to pay the family compensation. The careless girl had to go to hospital because she had spinal deformation" Mycroft wistfully glanced at his umbrella.

The two men were silent for a moment, processing this mystifying knowledge.

Mycroft then broke the ghostly silence that wasn't normal for John or Mycroft. This was new territory for them both. "John, the strange thing was that Sherlock's name was on the check. It seems suspicious"

"Maybe he is trying to pay for the family, since he feels sorry for the girl?" John said confused "But why would he do that? He is Sherlock Holmes. Who knows what goes on in that strange head of his"

"I have no clue" Mycroft said "Perchance someone might have forged a cheque with Sherlock's name on it, but the cheque seemed legitimate." Mycroft seemed to go off in thought.

"Mycroft, you are probably over thinking it. The man probably black mailed Sherlock into forging a cheque for him." John theorised

"Thank you, John. I've never despised a man before and I don't know why" Mycroft said

Both men were silent for a while, thinking about the accident that happened not that long ago.

"Anyway. I'd better be off. Work is calling. Goodbye John, see you soon" Then he morosely walked to the Diogenes Club.

"Goodbye Mycroft. See you soon" John said turning around to wave at Mycroft who barely twirled his crippled umbrella as a goodbye, without turning around.

Soon after Mycroft was out of sight, John glanced at the door to Sherlock's house, for a moment John thought about talking to Sherlock. Soon after he realised that Sherlock would barely talk and it would be a waste. At that instant, John headed of to the home he and his wife, Mary shared.

 _Authors note:_

 _The first chapter of my new Fanfic! SlightlyStrangeGirl has already read this, she said it's good._

 _Whenever I will post a chapter, I will have already written the next chapter. I will always be a chapter ahead. Just in case I have a writers block, there will be an update._

 _This fanfic is based on_ _ **Robert Louis Stevenson's The Strange Case of Dr. Jekyll and Mr. Hyde.**_ _If you have read it, please don't spoil it for anyone who hasn't read it! Thanks! There will be roughly 10 chapters! I do not own Sherlock, the BBC does._

 _People who review can get a sneak peak of the chapter! It's not bribing! I do live in the UK, so they might be a few hours or so after you post a review! :)_

 _I do have a Sherlock one shot up. It's about Sherlock and Trains. :)_

 _This was posted yesterday (31/5/15), but it came up with codes, I had to replace it! Sorry for the confusion! :(_

 _-TwilightMortal_

 _xx_


	2. Chapter 2: The Pursuit Of Moriarty

**The Troublesome Tale of Sherlock and Moriarty**

Chapter 2: The Pursuit of Moriarty

 _Previously on The Troublesome Tales: At that instant, John headed of to the home he and his wife, Mary shared._

Chapter 2:

When John got home, he found Mary reading the local newspaper, a habit she had picked up from John over the time they had been together.

"John" Mary said lovingly "How was fish and chips with Mycroft? Discuss anything interesting?" She asked

"Just about the attack on the teenage girl that happened not so long ago" he said, dismissively.

"Yeah, I heard about that" she said, looking around from the corner of the arm chair she was currently sitting on.

"Sherlock's name was on the check." John said simply, while he made himself a cup of tea

"Sherlock? Why would he do that?" Mary asked curiously, Sherlock didn't talk to anyone. So why communicate with a criminal of all people?

"No one knows what goes on in that head of his" John said sighing, picking up his favourite mug to walk over to where Mary was sitting. He sat himself down on the opposing chair.

He took a sip of his tea. Looking longingly into the distance, remembering the days when the hardest times of his life in the war, now just a mystery that Sherlock had dragged him into.

Sherlock had changed. And John knew he was right.

~OooO~

A few days after John's strange conversation with Mycroft. A will and testament of his reclusive friend; Sherlock came through the post. John pulled the letter out of the packaging. It read that _'If Mr. Sherlock Holmes died or disappeared for over three months, everything would go to Mr. James Moriarty.'_

That name. It seemed familiar to John. To familiar for comfort.

Recently, Mycroft had found out the name of the "Criminal", it was James Moriarty. Why would Sherlock let a criminal take over his life and work? This question boggled John's mind while he worked that day. His patients had to keep snapping their fingers to lure John back to reality. The reality that he didn't want to face.

~OooO~

Later that night, John wearily sat down on his worn out chair, thinking about Mr. Moriarty. Soon, he gave up and grabbed the TV remote and switched on the 32" television. John switched it on the local news to find out that Moriarty had been busy. Very busy indeed.

He had blown up some houses with people still inside. How could a man do this? Did he have a conscience?

The reporter warned everyone that Moriarty was out there, the police could not catch him.

Moriarty seemed to clever to be caught. Criminals were normally not that smart. Something seemed wrong. The answer was just hanging in the air, waiting for someone to put the pieces together.

John needed answers desperately. He had wondered if Moriarty had some knowledge over Sherlock, so he could blackmail him into forging cheques or helping him cover his tracks. John first wanted to talk to Molly Hooper; A scientist at Bart's hospital who is also Sherlock's friend. She would be able to help him and maybe she could go to Sherlock and hopefully talk to him.

John did this for two reasons. One was for answers and that most people can see that Molly likes Sherlock, as it is clear as a bright day with no clouds.

~OooO~

"Hello John, how can I help you?" said Molly enthusiastically as John walked through the lab door.

"It's Sherlock" John said, unsure of how she would react

"Ohh" she said

"Have you spoken to him recently"

"No" she replied to quickly

"What happened?" John asked sympathetically

"We had a disagreement over a part of scientific discovery. What he was asking about is unheard of." Molly said sadly

"Oh, I'm sorry."

"You don't need to be sorry. Why would you be?" said Molly, she glanced back at her microscope, she was trying to figure out how a middle aged woman died of a peculiar type of spots that Molly had never seen before.

"I brought up Sherlock" John said reluctantly

"Sherlock seems to be acting strangely lately and I wondered if he was acting strangely towards you" she asked, avoiding John's worried gaze.

Thinking that Molly felt like she wanted to be alone, John left.

~OooO~

Later that night, John was haunted by terrifying nightmares in which a faceless man battered a teenager to an almost death. In which the same terrifying, faceless figure stands beside Sherlock's bed and commands him to awaken. John sprang up in bed, he wiped the sweat from his forehead. The dreams felt too real, like they were about to happen but John wasn't a fortune teller, he was far from it.

After those creepy dreams, John had begun to search for any clue about this mysterious figure that haunted him day and night. John wondered if Sherlock would like to help him hunt down this murderer, John had asked Sherlock but he declined due to scientific experiments that needed his urgent attention.

So, John turned to Mycroft, Mycroft gave him many details about the man, such as his address, his bank details, his birth certificate and his medical files. Which Mycroft gracefully gave him with no questions asked.

The only normal thing about the man, was that the house that he resided in was bought about a few weeks ago that he had bought himself although he didn't seem to have much money, not enough to buy a house. John considered that Moriarty could have stolen some cash here and there, not enough to bring the police on him, but enough to eventually buy a house. Moriarty seemed to brilliant to steal, John considered him to be smarter than that.

The oddness about this criminal was that his bank details, medical files and birth certificate were recent. This man looked around his early thirties. He didn't look that old. Surely, these details weren't forged, they looked too real. Honestly, wouldn't he want them to look convincing? John knew the police would be fooled as they were not that smart, Sherlock always said that they wouldn't see the real criminal unless they were staring them in the face and saying "I'm the criminal" but sometimes even that wouldn't force them to search in the right direction.

John decided that he wanted to do something. He was going to find Moriarty and ask for some answers. Mycroft normally wouldn't ask John to literally stalk a man but he did. John was going to stalk Moriarty.

~OooO~

Moriarty was living in a more criminally active part of London. John seemed slightly nervous about going there but he had gone to places far worse, like that damned drug den.

Later that night, John went out into the darkness of the night and search for the elusive Moriarty. John began his search near the run-down building where Mycroft saw Moriarty enter, in the hopes of catching a mere glimpse of the man that was Moriarty. It was also near where Moriarty lives. It was the place where the criminals came to live after they had been released from prison. James Moriarty didn't have a criminal record, but not yet anyway.

~OooO~

Just as John walked around the corner, he saw a man walk up to a house, it was Moriarty! John almost jumped with joy and fear. He had almost bumped into a criminal or a murderer. John tried to shake off the fear that clearly littered his face. During his fear elimination process, Moriarty had snuck off.

"Wait!" John almost yelled, John didn't want to be seen with a murderer. He bounded up to the man with haste.

"Hello, is it James Moriarty?" John asked, he voice came in short breaths, he was breathless from trying to catch up with Moriarty, he walked so quick. "I'm John Watson, I'm friends with Sherlock Holmes."

Moriarty looked to the ground as if he was regretful.

"Hello, John Watson, I'm Moriarty" he said in a quiet but cheeky voice "Its a pleasure to finally meet you" John could see the corners of Moriarty's face turn up into a small but devil-like smile.

"Can I please see your face? I know it sound really odd, but it's nice to meet you to. I would like to be able to recognise you if we meet again" John asked, he wanted to make a good first impression and not scare him away.

Moriarty hesitated but he complied "Fine" he grunted, he seemed like he didn't want to, but was compelled to do so.

John was appalled and horrified, although he couldn't pinpoint exactly what makes Moriarty so grotesque and disgusting.

Moriarty was not easy to describe. There was something wrong with his appearance; something offensive, something utterly detestable. John had never saw a man he had so disliked, even more than Magnussen and yet he didn't know why. Moriarty had be deformed somehow; he gives a strong feeling of deformity,

"Here is my house, so if you need anything please come and see me but I might not always be here. One day, I will be here every day, these days I am so busy" Moriarty had said that too quickly, John interpreted this as a sign that he eagerly anticipated the death of Sherlock and the execution of his will. Moriarty seemed to want to take over Sherlock's life, but John had a feeling that this was right, he didn't know why.

~OooO~

After this encounter with Moriarty, John wanted to pay a visit to Sherlock, since Sherlock always knew what to do. He knocked at the door to 221B Baker Street, but he was met by Mrs Hudson, Sherlock's elderly landlord that kept thinking he was gay.

"John, how nice to see you" she said with delight in her voice

"Hello. Umm, is Sherlock here?" He asked

"John, come in, it's cold, you don't need to stand by the door." She said humbly

John followed Mrs. Hudson into the flat, they went up the creaky stairs, John wanted to expect to hear the sounds of Sherlock's violin echoing throughout the flat but it was deadly silent.

"Ohh. He isn't here" John said, he felt a tiny bit awkward."Moriarty was here a while ago. Sherlock gave him a key." She said, grabbing the feathers duster to finish what she had started before John had arrived.

"He trusts Moriarty?" John said, confusion entered his brain, it messed everything into a heap of unanswered questions and answers that had fallen apart with a little piece of new information.

"Yes. Sherlock has asked me to treat him as a welcome guest." Mrs. Hudson said as if it was to be expected.

"He has?" John said, confused at these words "I have to get home now. Mary wants to see me" John rushed off, Mary didn't want to see him, it was just an escape card.

Sherlock? Trusting a criminal? Things definitely didn't add up.

John had to confront Sherlock about this. He didn't know where to look. John had gone out looking for answers but ended up needing even more.

 _Authors note:_

 _Hello. Any questions? I bet you have many! Mwwhahaha!_

 _Hello Molly, Mrs Hudson, Mary and finally Moriarty! Next chapter we meet Sherlock! Maybe Lestrade and Anderson! Who knows…_

 _This is set after season three, but there was no 'Miss me?' from Moriarty. Also, why do they keep pushing back the date of season 4? Stupid BBC, why taunt me? Anyways, enough of that!_

 _Sorry about the delay, I keep_ _procrastinating about doing this. Sorry! :( I will try to be quicker in the future. The updates will not be weekly as I'd hoped, I will try to figure out when I will update. By now, I have a rough draft off the next chapter. So reviewing gets a sneak peak.._

 _Oh, reviews, thank you SlightlyStrangeGirl for my_ ** _only_** _review. Please review, every single one makes my day a whole lot happier! :)_

 _I've gone on for too long, sorry again._

Disclaimer: I don't own anything! I wish I did. Doesn't everyone? It would get season 4 done a whole lot quicker!

 _Remember if you review, you will get a sneak peak of the next chapter, it would magically appear in your inbox, a few hours later. It works like magic!..._

Until the next chapter! :)

 _-TwilightMortal_

 _xxx_


	3. Chapter 3: Sherlock Was Satisfied

**The Troublesome Tales of Sherlock and Moriarty**

Chapter 3: Sherlock was satisfied

 _Previously on The Troublesome Tales: John had to confront Sherlock about this. He didn't know where to look. John had gone out looking for answers but ended up needing even more._

Chapter 3:

 _Two weeks later…_

Sherlock was finally back to being himself, or so John thought.

John couldn't be more happier. Lestrade had been struggling with a confusing case. A man was found lying face down on the floor but dead in a room with no weapons and no signs of a murder or a struggle. The man was found dead in his house by his distraught wife.

She had only just popped out of the house to buy some milk from the corner shop, that was just down the road from their tiny little flat, in North London. Nothing that would help Lestrade in any way with the confusing case. That was true until Sherlock saved the day by appearing spectacularly down at the precinct of London Yard.

Lestrade had almost cried with happiness when he saw Sherlock's face, he had immediately called John and asked him to meet them at the crime scene. John was more than delighted to hear that Sherlock was there to help, but also John could finally talk to him. They hadn't spoke for months. Which was unusual for Sherlock, normally he texts John to help him on a case.

 **~OooO~**

"How long he been dead?" Sherlock asked, peering down at the body of the man lying there on the carpet.

"No blood or any weapon that would indicate any form of bruise or broken bones or murder." Sherlock says as he walked around the corpse, looking for anything that would help him determine how the man died.

"His name was Cameron Smith" Anderson said he walked through the doorframe glancing at the ID that was found on the dead man's corpse. "He was lawyer, a good one as well. Everyone adored him, no one would want a man like that dead."

"Shame" Sherlock said too quickly to show signs of sympathy, Sherlock was analysing the corpse with a plethora of exceptional detail. All eyes went to Sherlock, he just carried on analysing the body, no one knew how he could be so heartless and insensitive.

"The man is dead, Sherlock show some respect" John said, he leant down to get a closer observation of the man

"Cameron Smith" Anderson insisted, frustrated that they keeping calling him 'the man', not by his real name.

"Shut up Anderson" Sherlock said "I'm trying to work"

John sighed, that feud will never get old, he thought, casting his mind back to when Sherlock first insulted Anderson. John knelt down to get a closer look at the body. He glanced at the corpse, looking for any medical symptoms, he could check for, that would help them to figure out how .

"Poison" Sherlock shouted, he was on to something "It is the only explanation. No clear signs of a previous stabbing or gun shot wound"

John remembered the case of 'The Bloody Guardsman' which the killer used the belt to bind the skin together after stabbing the intended victim. There was no signs of this, Sherlock had checked the body several times.

"I need to go to Barts, I need to test the blood for poison" Sherlock said as he promptly collected a sample of blood, then swiftly left the room with Bart's hospital in mind.

"Molly" John breathed. She was still angry at Sherlock. Maybe his complete turn of heart will affect her as well.

John hoped for the best, or he would be stuck in the middle. A bystander. A third wheel. He would be a lonely third wheel.

 **~OooO~**

Sherlock sauntered into the lab to find a bemused Molly who was working on some cells that were under her microscope.

"Sherlock" she said simply, with no emotion. She turned back to her microscope and then she carried on working. She still hadn't figured out those irritating spots.

"Hello Molly, nice to see you" Sherlock said, oblivious to Molly's heated expression.

Tension had dispersed through the room like wildfire, it was everywhere in the small time that was a few meek seconds. It only confused John immensely as he still didn't know what they were feuding over. He wanted to ask, but it would stir some sentiment

Sherlock had found the necessary equipment to analyse the man's blood for any form of poison. He placed the microscope on the table and put the blood on a dish and started to examine the blood sample.

Sherlock was silent while he analysed the blood, as he could enter his mind palace to recognise the poison as soon as he could.

Sherlock's silence gave John time to reflect over Sherlock and his faultless turn around.

 **~OooO~**

The previous days, no one had seen Sherlock as he was in hiding for reasons unknown but over night he had made a full recovery, he was back into being himself. People cannot change behaviour that had developed over months, Sherlock is quite changeable. He can be serious about a murder but then materialise into being thrilled when Lestrade had comes to him for his help.

But this, no one that John had ever encountered so far, can change that much, in one night. It was a curse near impossible.

Lately, for John, the impossible is changing into the quite possible.

 **~OooO~**

"Cyanide" Sherlock exclaimed, he had almost jumped in joy.

"What?" John said, standing up, he recognised the name but he couldn't remember what it was. All John knew was that it was dangerous, it had just killed a man.

'After examining the blood sample, Sherlock had shifted aside the microscope he had used so he could infiltrate his extensive mind palace. John still had no clue why it was a _mind palace_. His guess was that a _palace_ seemed more sophisticated, more than a simple mansion.'

"Cyanide is a mitochondrial toxin that is also the fastest lethal poison known to mankind." Sherlock articulated "Cyanide ion halts the cellular respiration"

"That is how he died?" John said, disbelieving.

"Why would anyone want to give a charitable lawyer, Cyanide?" John reckoned "Besides, how would anyone buy this lethal poison? Who would sell this?"

"It is the perfect murder weapon" Sherlock said, avoiding the John's questions. "Cyanide can cause death within minutes to hours of detection. Significant cyanide is highly uncommon. It has to be noticed quickly to ensure prompt and proper administration of life saving treatment"

"Wow" John said, he felt like he would be blown away. A benevolent lawyer, with no known enemies, was poisoned with a highly lethal poison. It made no sense to John, but nothing made any sense now anyway.

 **~OooO~**

"It was Cyanide" Sherlock explained

"Cyanide?" Lestrade said confused, he also had no clue what the poison was.

John tuned out Sherlock's lecture, he has already listened to Sherlock, no more than half an hour ago.

Once Lestrade had been informed, Sherlock left the building, he held his hand up. He was trying to hail a cab. Luckily, a cab was near, Sherlock seemed in a hurry to return home.

"221B Baker Street" Sherlock said clearly to the driver as he got in to the vehicle.

"Sherlock, I need to talk to you" John said as he settled himself into the cab, he closed the door and the cab started its journey to 221B Baker Street.

"About what?" Sherlock asked

"Your will" John said simply

"My will? I sent it to you, I knew you would keep it safe"

"Why write it now? Why not later in life?" John said cunningly, trying to extract crucial information from Sherlock, which could ease John's enthusiasm to solve the case from Mycroft about Moriarty.

"John, no one knows when they will die. Better to have one as soon as possible" Sherlock said, he almost smiled but it seemed to pessimistic.

"Anyway Sherlock. Why have you included Moriarty in your will? You barely know him"

Sherlock didn't answer.

"I have been learning something of Moriarty, he seems very unusual" John said looking in the direction of the dusty floor of the London cab. John refrained from calling Moriarty a 'Troglodyte', it seemed right to call Moriarty a troglodyte but it also seemed merciless. To stay on the safe side, John didn't speak his mind.

 **~OooO~**

Out of the corner of John's eye, he could see Sherlock's face turn ghostly white. Sherlock was hiding something. It had something to do with Moriarty. Maybe John's theory of black mail was true or it was Sherlock being forced to help Moriarty. Either way it was sinister.

After a few minutes, Sherlock recovered from turning ghostly white.

"John, I feel… obliged to help Moriarty. He is a struggling mastermind with no direction in life." Sherlock said, what he was saying didn't seem like it was Sherlock's choice of words. It wasn't something he would normally say.

"The situation with Moriarty is exceptional" Sherlock trailed off "It cannot be solved just by talking." Sherlock knew something about Moriarty, but he wasn't letting John know.

Sherlock was hiding something, something sinister. John hoped it wasn't as bad as he thought. Sherlock claimed to love solving mysteries that no one else could solve, but now, he himself was turning into one of those unsolvable mysteries.

"John, the moment I chose. I can be rid of Moriarty." Sherlock mentioned

"Okay" John said quietly. That was not at all what John was expecting to hear.

"John, If I ever disappear please look after Moriarty, I fear he is lonely and in need of help. Please carry out my will when I am not around to help"

"Sherlock. I promise" John said seriously, John would carry out Sherlock's will but if Moriarty did turn out how John thought he would, the promise that John made would become void, but John felt honour bound to Sherlock's will, he was Sherlock's friend after all.

 **~OooO~**

The cab finally pulled up in front of Sherlock's house, after a few minutes of uncomfortable silence.

"Thank you" Sherlock said as he got out of the cab. John followed him out of the cab. John almost slammed the door with frustration. John sighed as the cab sped away.

Turning around, John looked for Sherlock, but he had already dived into his house, without saying goodbye. Was Sherlock in need of finishing a experiment? But he had gone to London Yard. He wouldn't have gone to London Yard in the first place, if he had an experiment to finish. Something was different.

Sherlock has changed. It really didn't seem like it was for the better.

 _Authors Note:_

 _More questions? Don't worry about that, they will be all be solved in the last few chapters! Mwwhaha!_

 _Sherlock's slight personality change at the end of this chapter is completely relevant to the story. In the final chapters, like I previously said, will all be answered._

 _Disclaimer: I don't own Sherlock. Boo hoo!_

 _All reviewers will receive a special sneak peak! All reviews such as positives and improvements are welcomed but no flames please, I will remove them and they will have no sneak peak! ;(_

 _At the moment, I have only two reviews, it is a bit disappointing, I can see how many people are reading this, but only SlightlyStrangeGirl reviews. (By the way, thank you!) Is there something wrong or bad about this story, I would love to hear what it is so I can improved it._

 _Reviews are my Fan-fiction life-line, they keep me writing, if I do not get many more reviews, I may just delete this story, there is no point writing something that no one likes. ;(_

 _There is a reason why I chose Cyanide. Anyone want to guess? Whoever guesses correctly I may send them a hint of who dies in the next chapter…._

 _I'm really sorry, but next chapter I will kill off a beloved main character. Please don't kill me,_ _heaps_ _of main characters will die in this fanfic. I really didn't want to, but it all goes perfectly with the story!_

 _I've said too much!_

 _Until next time!_

 _-TwilightMortal_

 _xxx_


	4. Chapter 4: Lestrade's Murder Case

**The Troublesome Tales of Sherlock and Moriarty**

Chapter 4: Lestrade's Murder Case

 _Previously on The Troublesome Tales: Sherlock has changed. It really didn't seem like it was for the better…_

Chapter 4:

 _One year later…_

From Lestrade's point of view:

Lestrade was walking home. He had finally cracked the Cyanide poisoning case. Of course, he had help from his friend Sherlock. He didn't know how he could have solved case without Sherlock.

There was an almost skip in his step, they had arrested Cameron Smith's killer. His name was _Charles Augustus Magnussen_.

 _Cameron Smith was Magnussen's Lawyer. He was losing the case, Magnussen was being convicted of blackmailing an innocent woman since he had illegal documents about her that he could use to convince her to do his bidding. But he had been caught. The woman was at the end of the line, she wanted the police to know what Magnussen was doing and how much illegal documents he had acquired over many years. Magnussen was then arrested and was taken to court._

 _Cameron couldn't help Magnussen in any way, the evidence was staring him right in the face. Magnussen was on his way to prison when he slipped Cyanide into Cameron's water bottle._

 _Now, Magnussen was being sent to court again but for murder._

A smile appeared on Lestrade's face. Recently, it had taken him week or even months to solve cases since Sherlock had isolated himself away from society, but now, things seemed to ascending. Sherlock had emerged from his self-incarceration and nothing could make Lestrade miserable now.

"Hello" he said to a random passerby

"Hello" the passerby said back

Both men stopped walking for a small chat, or so it seemed…

"How are you?" Lestrade asked

"I think a better question is 'how are _you_?' " the passerby said, Lestrade looked at the man with a quizzical look. The passerby was wearing a long dark coat with a black top hat.

"Huh?" Lestrade said, still confused

The passerby then pulled out a gun and shot Lestrade in abdomen three times.

Lestrade whimpered in pain but then he was shot in the head, instantly killing him. His body fell to the pavement and his passerby walked away with an evil glint in his eye. Without realising his gun fell to the ground, it stayed by Lestrade's corpse.

A woman was peering out of her bedroom window, gazing out at the night sky, she had witnessed the shooting, she screamed as she saw his body fall, she feinted from the sights of blood pooling out from the gun shot wounds.

Back to John's point of view:

After his long day with Sherlock solving a case, John had gone straight to bed, sleeping soundly. He had awoken from a dreamless sleep by Mary.

"John wake up!" Mary said, trying to drag the covers from him, but the unconscious John didn't want to let them go.

"What?" he moaned, sleep still trying to bring him back to unconsciousness, but John fought to hold on to the consciousness.

"There has been a shooting" she said, sadness seeping into her voice

"Where?" John sat up, curious at the mention of a shooting. John seemed to be fully awake and alert.

"Near Baker Street" Just these three little words sent John into a full-blown panic attack.

"Sherlock?" John said soundlessly, he was unsure of where this was going.

"Lestrade, he was shot last night. He was shot multiple times in his stomach but then shot in the head" Mary got quieter as she finished her sentence, she knew John would stop listening once he knew Lestrade had been killed.

"Lestrade w-was k-k-killed" John said, his voice wavering due to disbelieving that his dearest friend was dead.

"You got a call from the other detectives at London Yard. They want you at the crime scene." Mary said wistfully

"Why?" he asked immediately

"They didn't say why" Mary said

John really didn't want to go to the crime scene and see his friend's dead body. He knew he wouldn't stop himself from tearing up.

John got up silently and readied himself to go to the scene. Mary silently walked around John as if she was walking on egg shells. She didn't want to upset John more. Mary felt terrible, she had broken the news about Lestrade's death to John, Lestrade was John's friend. She didn't want someone else telling John.

 **~OooO~**

"Lestrade left London Yard about eight last night. We guessed that he was murdered on his way home, we estimate that his time of death around quarter past eight" Anderson said

John noticed that all the detectives and police offers were working slower than usual. It was to be expected. Lestrade was their friend, their work colleague. They were working on his murder. It must have been terrible to learn that he had died, then realising you have to work on the case. John's heart went out to them.

John walked around the crime scene, looking for Lestrade's body. Part of him wanted to see him one more time, the other part wanted to leave the scene immediately. He chose the first option. He wanted to say goodbye.

The sight of Lestrade laying helplessly on the ground with a large pool of blood surrounding him was devastating. John clapped a hand to his mouth. He should have listened to his conscience and stayed away. John shouldn't have seen his friend this way. It has affected John's last memories of Lestrade,

 **~OooO~**

"This must be the killer's gun" said Anderson, appearing with a gun "It is the right size for the bullets. Also, why would someone randomly leave a gun next to a dead body. I will get it checked for prints"

John could picture Sherlock saying 'Well done Anderson, you have actually used your brain for once' but Sherlock wasn't here. Where was Sherlock? John wondered. He looked around the crime scene. Only seeing weeping investigators, who were crying over the body that they had to examine.

Sherlock didn't come to solve his friends murder? Wouldn't he want to find the killer? Wouldn't he want to avenge Lestrade's death? And get justice for the murderer?

While John was searching for Sherlock. Anderson appeared yet again, but with a woman.

"What now Anderson" John hissed

"John, this woman witnessed the murder." Anderson said calmly

"Hello, I'm John Watson" he said, turning to the scared woman. She looked like she was in her mid twenties. She had long blonde hair that was pulled up into a high ponytail and her bright blue eyes were clouded with fear.

"I-I. My name is Katerina Taylor." she announced, she hesitantly shook John's out-stretched hand.

"What happened last night" John said sympathetically

"Your friend.."

"Lestrade" John said

"Lestrade, he um.. was walking happily down the road. Then he got talking to a man, he was wearing a long dark coat with a black baseball cap" Katerina paused "Then the mysterious man pulled out a gun shot him in the stomach then in the head. He dropped the gun. I cannot remember much more than that. I'm sorry, I must have feinted. There was a lot of blood. I cannot stand blood at all." she started to cry into a small tissue that she kept clasped in her tiny shaking fingers.

"Thank you for your statement Miss Taylor" Anderson said compassionately "You can leave now."

"Thank you" she said, before she dashed off back to her house.

 **~OooO~**

"The prints just came back." Anderson said, returning to John again.

"Who?" John asked eagerly, wanting to know who the killer was.

"James Moriarty" Anderson said

Moriarty murdered Lestrade. Sherlock knew Moriarty. Surely Sherlock would abandon Moriarty once he knew Moriarty had murdered Lestrade for no reason.

After a minute of silence, John finally spoke "I know his address" he said

"How?" Anderson wondered

"Long story." John said, wanting to avoid the truth. He grabbed a piece of paper out of his coat pocket and wrote down Moriarty's address and gave it to Anderson.

He looked at the piece of paper, then turned back to John.

"Thanks" Anderson said , before he started to walk away.

"err. Anderson. Can I go too?" John asked

"Sure" Anderson said, he turned around with a strange smile of confusion on his face.

 **~OooO~**

On the long road to Moriarty's house, John speculated how a man like Moriarty could be successor to everything. He would become Sherlock after he 'dies or disappears', but why would a criminal take over a detectives life? Normally, a detective discovers who commit a crime and how they completed the crime. Why would Moriarty help the police to find out how he had killed a man?

The car finally pulled up at Moriarty's house, which brought John out of his daze.

A police officer gets out of his vehicle and rushes up to the rusty door. A wicked-looking elderly landlady opened the door. Both the Landlady and the officer talk about something that John couldn't hear. He could only guess that the officer was asking to search the residence. The office then turned around to beckon the other officers inside to hunt for the fascinating criminal that was Moriarty.

Every single police officer runs into the aged house. The landlady was shocked, she had no idea why they had disappeared into the house.

John waited in the car, waiting to see what they would find. John hoped that Moriarty would be caught, then Sherlock would be himself again. John still hadn't received some much needed answers about Moriarty from Sherlock.

A few minutes later, they all came out. Each officer had a solemn look that covered their faces. All they found was the burned remains of an tired and old chequebook. Who uses cheque books these days? Moriarty must have a bank account, if he burned the cheque book, he might need to withdraw money.

With police officers stationed at every bank in every possible bank Moriarty could go to, they waited for him to turn up. All they had was time. They would get him in the end. No matter how long it took.

 **~OooO~**

Numerous days and weeks passed, no sign of Moriarty. Where could he possible go? There is no where he could go. His house and his local bank are being monitored. Where could Moriarty go? He has no friends that John knew, apart from Sherlock, Sherlock wouldn't hide a criminal. Moriarty couldn't disappear into thin air. It was _very_ unlikely.

But all signs pointed directly to Moriarty disappearing of the face of the earth. Where could a man go to in his darkest hour of need? Every police officer is alerted to catching him and bringing him to justice.

All John knew was that Moriarty has no family, no friends, and those who have seen him are unable to give accurate descriptions, differ on details, and agree only on the corrupting aspect of Moriarty's appearance.

 _Authors Note:_

 _Sorry about killing Lestrade! I had to kill someone, unfortunately, it turned out to be Lestrade. In my opinion too many people die in the original story of Jekyll and Hyde, so I have to kill the same amount of characters!_

 _I am able to update quite a lot recently since I have barely any homework *jumps in joy* and it is the weekend. During the week, I can't write a full chapters each night. So I might be able to update on Wednesday or Thursday, maybe even earlier! Just wait and see…._

 _I have never been to London, so I have no clue about road names or anything like that, so I didn't include a road name._

 _Any more questions about this mysterious story? *Smiling evilly and wondering if 'evilly' is an actually a word*_

 _Luckily, no one is killed next chapter, but in the_ _sixth_ _chapter, another beloved character dies. This time, I wish I wasn't going to kill this character, but sadly I will kill him or her!_

 _For this story, Anderson still has his job. I didn't want to use an OC, so I used Anderson._

 _Disclaimer: BBC owns Sherlock, I wish I did, then season four would already be out. Dreams, sweet dreams…._

 _Reviews have changed. Thank you to SlightlyStrangeGirl, Chocchops, Mango2001, Rubix12 and Rainy2092. You have all made my day! :) Reviews keep me writing, they are my fan fiction food! ;)_

 _Until next time,_

 _-TwilightMortal_

 _xx_


	5. Chapter 5: The Episode Of The Letter

**The Troublesome Tales of Sherlock and Moriarty**

Chapter 5: Episode Of The Letter

 _Previously on The Troublesome Tales: Where could a man go in his darkest hour of need? Every police officer is alerted to catching him and bringing him to justice. All John knew was that Moriarty has no family, no friends, and those who have seen him are unable to give accurate descriptions, differ on details, and agree only on the corrupting aspect of Moriarty's appearance._

Chapter 5:

The next day, John decided to go to Sherlock's house to talk. John needed to talk with his friend. Everything was getting so confusing lately. John wanted to clear his jumbled head. He wanted- _no_ _needed_ to clear his head. Everything was out of place, but John was not a neat freak.

~OooO~

When he opened the front door, he slowly walked up the creaky stairs and went through the door at the landing. He was surprised to see Sherlock sitting on the leather sofa, smouldered in blankets from the kindness of Mrs. Hudson, looking deathly ill. John feared for Sherlock's health, he looked at death's door.

"Moriarty has left." he said feverishly, he shivered before each word that he spoke "I will no longer help him. Not any more."

"Why?" John asked, only a few days ago Sherlock had asked him to help Moriarty. Why the sudden change of heart?

"It doesn't matter, John" Sherlock said, he was trying to escape the mountain of warm blankets.

"The police are after him, Sherlock." John said soothingly, but nothing seemed to calm down Sherlock "Whatever he has done to you, he _will_ be brought to justice"

"They will not find him." Sherlock looked John right in the eye as he spoke, conviction was clear in his feverish voice

John wanted to ask why, but Sherlock kept speaking.

"The police shall never find that abhorrent man" Sherlock said, hatred trickled into his voice. Sherlock definitely hated Moriarty.

 _'_ _Join the club'_ John thought sarcastically.

Sherlock hastily grabbed a scruffy piece of A5 lined paper from the table in front of him and tried to give it to John, but he seemed of in thought.

"This letter came a few days ago." Sherlock said, before burying his face into the blankets "It is from Moriarty"

John's attention flared at the mention of Moriarty. He took the letter from Sherlock. It read:

 **'** _Sherlock,_

 _I have a method of escape if all goes wrong, do not worry about me. I am no longer worthy of your greatest generosity. Thank you for everything, you were so generous. Do not worry about me anymore, Moriarty x.'_

"What shall I do about it John?" Sherlock said worriedly "It could damage my reputation."

"Did Moriarty influence your will? Or anything?" John demanded, he was beyond mad at Moriarty "…Especially that he would inherit your life in the event of your disappearance?"

"Yes, yes he demanded that I write him in the will. How could I be so foolish?" Sherlock said sadly.

Something clicked into place. _Finally_.

John realised that Moriarty's end game was to murder Sherlock and take over his life, but the police wouldn't catch him. According to Moriarty, in his letter to Sherlock he mentions that he has a _'method of escape if all goes wrong'_.

John wanted to find out more about this Moriarty and how he could have any interest in Sherlock. Why would a criminal want to take over a detectives life?

"Can I please take the letter?" John asked, he stood up, he was ready to leave and find Moriarty to bring him to the justice that he so deserved.

"Sure" Sherlock said immediately "I do not want it."

"Erm.. thanks" John said confused at the usual behaviour of his best friend. At least, he was talking to his friends again, not hiding himself away like a contagious disease.

John walked out of the room, towards the stairs when he almost walked into Mrs Hudson.

"Hello John, nice to see you" Mrs Hudson said cheerfully.

"Mrs Hudson? Did you seen anyone post a letter for Sherlock a few days ago? Was he wearing a long black coat?" John asked

"No, not really." she answered, trying to remember back to the last few weeks. This led John to believe that Moriarty could be quite undetectable, although nothing normally gets past Mrs Hudson.

~OooO~

That night, John and Mary were watching the news. Mary actually watching to find out what was happening around the world but John was trying to forget his problems and worries.

"Sherlock got a letter from Moriarty" John said casually as he ate his meal, that was balanced on his lap.

"Really?" Mary said astounded.

"There was something familiar about it. I cannot think what it is" John said, he was frustrated that he couldn't see something that was right in front of him. It was almost driving him insane.

"Let me have a look" Mary suggested, seeing John's blank facial expression.

"Okay" John said "Why not?". He got up and walked over to his coat and grabbed the letter from inside his pocket and gave it to Mary, who immediately started to examine.

She read the letter, then started to look closer. After a few seconds of analysis, she got up. In search of something.

"Mary" John said as he turned around to look at her "What are you looking for?"

"A note from Sherlock" she said.

"Why?" John asked curious at why Mary would need a note from Sherlock.

"Remember how you said that Sherlock could be helping Moriarty?" she announced.

"Yes.." John said, remembering their previous conversation.

"Well, Moriarty handwriting is similar to Sherlock's own handwriting."

"Really?" John asked dumbfounded, his eyes were almost out of their sockets, due to the reveal of this surprising news.

"Ahh" Mary said, she walks back to John with another letter, this one was from Sherlock.

"Look closely John" Mary said, showing John the two letters. Nothing seemed similar, maybe John was overreacting. Maybe Sherlock had nothing to do with Moriarty.

"Moriarty's handwriting is the italic version of Sherlock's handwriting" Mary mentioned. John could not believe this. He didn't want to believe this but this was the answer that was hanging directly above his head that he couldn't see. Now, he could see this.

Now that John could see this new information. He could clearly see that Moriarty's handwriting _is_ leaning in the opposite direction, as if for the justification of concealment.

Anyone that knew Sherlock or had seem his handwriting before and then compared it to 'Moriarty's' handwriting, then it was as clear as day.

Alarm bells rung loudly throughout John's head. Sherlock was and is helping a criminal. The same criminal that murdered his friend. To add to this horrifying realisation, Sherlock straight line lied to John saying that 'it is from Moriarty'.

But Sherlock, was not helping Moriarty. John didn't know why but he was glad that Sherlock had finally renounced Moriarty. John could have jumped in joy, but he had contained it to a mental celebration.

Was he finally developing a mind palace? Sherlock would be pleased.

Although, Sherlock could be lying. John couldn't see right from wrong now. It was very hazy, like the fog in the mornings of wintery days in December.

On the other hand, Moriarty could have similar handwriting to Sherlock. It could be a pure coincidence. John wanted the latter to be true. He didn't want Sherlock to be aiding a murderer who he claims to hate.

Would Sherlock forge a text from a murderer? The real question was: Why? Why would Sherlock forge a text from a murderer? Why would he help Moriarty in the first place? There were so many questions involving Sherlock that begun with 'why'.

~OooO~

The next day, John decided to call Mycroft and tell him about Sherlock.

"Hello John" Mycroft said joyfully.

"Mycroft, have you recently heard from Sherlock?" John queried.

"Not in months." Mycroft said "But, I do hear that he is back in business. Whatever you said to him must have helped him get out of his mind palace."

"Recently, he has gone back to being secretive and reclusive."

"Sherlock is back in his mind palace?" Mycroft said "Shouldn't you be helping him?" Mycroft said grievously, with a hint of mourning. He was losing his brother. It was to be expected.

"Then Lestrade died." John said solemnly.

"Yes, I heard about that" Mycroft said.

"Sherlock. He didn't appear at the scene. It was the day after the case that he helped Lestrade solve."

"Interesting" Mycroft said "What is up with my little brother? One instant he is sleuth solving baffling cases, then he turns reclusive."

"It is all so confusing." John said, perplexed at Sherlock and his dysfunctional behaviour "I wish I know what is happening."

"At first, it seemed normal. For Sherlock after that point in time, it got discriminative." Mycroft said.

"I will find out what is happening with Sherlock, Mycroft. Even if it kills me. I need to know." John said, he was determined to know. It was why he got involved with Moriarty in the first place.

Firstly, Moriarty just seemed like a freak of nature who cared for no one but himself. A selfish, consulting criminal, who loved to blow up houses and kill people for no reason. Soon after, Moriarty had got involved with Sherlock, that was the end of the line for John. No one messes with his friends and gets away with it lightly.

"Thank you, John. Sherlock needs you to help him get his life back on track, even if he doesn't admit it, he needs you" Mycroft said.

"I'll help him, Mycroft" John promised "You have my word."

"Thank you. Goodbye" Mycroft said before he hung up the phone.

John put his phone down and put his head in his hands. How would he get Sherlock back? It seemed impossible.

But John would try anyway. Sherlock was his friend. His only friend. Sherlock was his best friend. And no one gives up on their friends No matter how long or hard it took, you would never give up on your friends. John wouldn't give up. He will help Sherlock.

 _Authors Note:_

 _GO JOHN!_

 _Ohh… What is up with Sherlock? Why is he so ill? Why has Moriarty just disappeared? Why has Moriarty left? Where did he go?_

 _Disclaimer: I will never own Sherlock. I want to, its a dream reality, that will only stay in a dream reality._ ** _DREAMS SWEET DREAMS!_**

 _This chapter was really hard to write as the original chapter was quite short, so I had to add more to it. This was why I was delayed in posting this. If it seems that I added things for no reason, tell me. I'm friendly!_

 _Next chapter, someone we all love dearly will sadly die! Then in the eight chapter, someone else dies and in the tenth and final chapter a few more people will die. I hate killing characters, but it feels so powerful. :D_

 _If anyone seems OC, please tell me, I hate making characters go OC, to me it feels out of place and Mycroft seems out of place to me. What do you think? Please tell me. :)_

 _The biggest question about Moriarty and Sherlock will be answered in the final lines of chapter nine!_

 _Thank you for the reviews. I really appreciate them! They make me feel guilty for not updating. So review galore, make me feel_ ** _really_** _guilty!_

 _I have no clue when I will update next, but it will be soon. (only 5 chapters to go!) We are half way through this story! I never want this to end._

 _ps. I am working on another story, its not Sherlock, I will give away nothing. Not to anyone! Mwhaha! Maybe in the future I will do another Sherlock story, or even a few one shots. Who knows? Not me!_

 _I've gone on for too long! Sorry! I'll end it here!_

 _Until next time,_

 _-TwilightMortal_

 _xxx_


	6. Chapter 6: The Adventure Of Molly Hooper

**The Troublesome Tales of Sherlock and Moriarty**

Chapter 6: The Exceptional Adventure Of Molly Hooper

 _Previously on The Troublesome Tales: Sherlock was his best friend. And no one gives up on their friends. No matter how long or hard it took, you would never give up on your friends. John wouldn't give up. He will help Sherlock._

Chapter 6:

Time passed and there was no sign of Moriarty, John was first angry that he had escaped but then his anger subsided when Sherlock started to get better, he looked like he would survive this terrible 'illness' that he was suffering from.

Sherlock started going back to normal. He was solving case after case after case. John had kept his promise to Mycroft and brought Sherlock to being himself. All was right in John's small world.

The removal of Moriarty's corrupting influence had a tremendously positive effect on Sherlock, which made John smile even more with happiness.

~OooO~

Two months after this peaceful lifestyle, Sherlock wanted to amend his relationship with Molly. So, he called both Molly and John to Barts to help him on a case, but they both knew that Sherlock didn't need help on a case but they went anyway. They wanted to see Sherlock.

They talked about possible causes of death.

"Stroke?" Molly asked.

"Could be." Sherlock said examining the body.

"Cancer" John said curiously.

"I've checked her families health records. No cancer" Sherlock said, he was ahead of John.

"Suicide?" John suggested.

"Really John? She did not die of suicide" Sherlock said "No signs of intentional injuries."

By the end of the night, they had found that the woman, who was in her early forties, died of a car crash incident that had occurred a week or so ago. She had apparently recovered but then all the signs and symptoms pointed to be a late stroke.

Sherlock was back to being himself. John was happy. John had forgotten his earlier worries of Moriarty and Sherlock's recently broken friendship with Molly was mended, and seemed stronger than it ever were.

~OooO~

A few days after the friends met at Barts, John went to see Sherlock. He glanced up at the door of 221B Baker Street, remembering the first time he saw that black door.

Then the door opened to reveal Mrs. Hudson, which instantly snapped John out of his vision of the past. How he missed it.

"Hello Mrs Hudson, how are you?" John asked out of a pure habit.

"Hello John, I am fine" she replied with a kind-hearted smile that John always associated with her.

"Can I see Sherlock?" John said hesitantly.

"Sherlock.. can see no one. He is very busy." Mrs Hudson said very quickly.

"With what?" John said confused, Sherlock seemed to be getting better, now it seemed, he was slipping back.

"A-a-an experiment" Mrs Hudson said stuttering, Mrs Hudson never stuttered. And Mrs Hudson never stuttered, something was up. "His experiment cannot be interrupted, he can see no more visitors."

"I'll be back later then" John said, walking back down the path. "Tell him that I had visited."

"I will. Goodbye John" she said, waving goodbye.

John walked away, in the direction of his house.

Something was happening, but he didn't know what and he didn't know if he wanted to know.

~OooO~

That same situation kept repeating every day, for a week. John was undoubtedly tired of going to Sherlock's flat and getting turned away yet again by Mrs. Hudson saying that Sherlock was busy with 'an experiment'. An excuse that John didn't believe now, he did for the first couple of times but then it got suspicious.

Questionably, did Mrs. Hudson know about Sherlock and the Moriarty incident? Perhaps, she did know, as Moriarty had free reign in Sherlock's flat.

After being turned away by Mrs. Hudson, John found himself at St. Bartholomew's Hospital, subconsciously he knew that he wanted to talk to Molly, to see if she knew anything about Sherlock and why he didn't want any visitors.

"Hello Molly" John said happily, as he burst through the doors to Molly's Lab.

"Hello John" she said weakly.

"Molly, wha-what's happened to you?" John stuttered.

Molly looked in a very poor health. She looked just like how John found Sherlock a week ago. Molly looked pale and sickly, with a frightened look in her brown eyes. What could have frightened her so intensely?

"I have seen a great shock, John." she said cheerlessly "I expect to die in a few weeks."

John was heart-broken. Molly was claiming to die. He couldn't lose another friend. Definitely, not so soon after Lestrade.

"Why Molly?" John asked.

"Life has been pleasant," she says, avoiding John's previous question. "I liked it. Yes, John, I used to like it." then she adds, "I sometimes think if we knew all, we should be more glad to get away."

"Okay Molly." John said sympathetically "Have you spoken to Sherlock, he may have had the same illness."

"This is no illness, John" Molly said with fury "Do not mention Sherlock. Do you understand?" she violently demanded, she had never shown this much anger before, it almost frightened John.

"I will Molly, I will not mention you-know-who" John said.

He was astounded to hear the fury in her voice, it was like she despised him. What had happened to Molly? The girl who liked Sherlock, but never admitted it?

"Me and Sherlock are no longer friends" Molly said, dejectedly.

"I thought you didn't want to talk about Sherlock?" John wondered.

"After my death, I promise that you may learn the truth about everything, but for now I will not discuss it." Molly said dolefully, ignoring John's question yet again.

"Goodbye Molly, see you soon" John said, trying to smile at her. He turned

towards the door.

"Goodbye John" Molly said joylessly.

~OooO~

When John got home, he wanted to ask Sherlock why he was back in hiding and what happened with him and Molly. He pulled out his phone and started to text Sherlock. He wrote:

 _'What happened with you and Molly? Why can I not see you?'_

John finished typing, he wondered how long it would take Sherlock to reply. But he sent the text anyway, he hoped and prayed that Sherlock would see this and reply. John put his phone on the table.

A few minutes later, John's phone rang.

Sherlock had replied.

 _'I care for Molly, she doesn't understand my motives at the moment. I understand why you are frustrated about not talking but I have to maintain a strict solitude, I cannot see anyone. I am suffering with a punishment that I cannot name. I promise that soon we can talk. -SH'_

John read the text, it was a long text, but Sherlock always wrote short and to-the-point texts. Something had changed. Will anything get back to normal? Would they ever change? What had changed Sherlock quite suddenly? Everything seemed like it was going.

~OooO~

A few weeks later, Molly died. She had fulfilled her prophecy. John was sad, another of his dearest friends had died. He didn't want anyone else close to him to die. It would break him and he wouldn't be the same again. He didn't want to turn out like Sherlock, hiding himself away because he had to 'punish himself'. John didn't want to become a recluse.

Molly had died a peaceful death. She had died in her sleep, a easy death for a kind woman. She didn't deserve to die this young, she could have done much more with her life. Why did everyone around John die? Did anyone else have to die?

But John, couldn't help wonder why Molly died. There was nothing wrong with Molly. She just looked deathly ill. Surely it wouldn't take longer for a disease to kill you. Could it?

~OooO~

"We are here to honour the life of Miss Molly Hooper." said the sorrowful pastor "She was a enchanting woman who died too young."

At that point John had stopped listening to the pastor who was conducting Molly's funeral. Like he knew Molly. All the pastor possibly knew about Molly, was most likely from stories from her friends.

"… as the caring forensic pathologist, she was always figuring out how someone died quite quickly. She was amazing at her job, no one was like her, no one could be her" said a teary colleague of Molly's, the poor woman was crying immensely, that she couldn't continue her eulogy for Molly.

John wondered if Sherlock would write a eulogy for Molly. Well, Sherlock did write a speech for John's wedding. John stopped in his tracks. Where was Sherlock?

John turned around. His eyes scanned the church. The only people here were Molly's friends who she worked with. John recognised no one. Sherlock didn't go. He didn't go to his friends funeral. Besides, Sherlock went to Lestrade's funeral, albeit that Sherlock didn't go to help out with the murder case.

John thought that Sherlock would want to pay his respects to someone who liked him, but there was no sign of the consulting detective. He didn't help out with Lestrade's murder, now he didn't turn up Molly's funeral. What was happening to Sherlock?

~OooO~

Back at home, John went through a stack of letters, trying to find a letter or bill. Or something to take his mind off the recent events.

At the bottom of the pile he finds a letter from Molly. That Molly wanted him to read after she died. Now that she had sadly died, he opened the envelope and read the letter.

Inside, was another envelope, it read: _'Not to be opened till the death or disappearance of Sherlock Holmes'_.

Why couldn't John read it now, Sherlock was as good as dead. John curiously wanted to know why. It was very tempting for John to find out what was in the letter but he had to do as the envelope said to do, so he put the letter on top of the pile. The letter was put away for safekeeping, John thought that he may need it soon, he had a feeling that he would.

~OooO~

Weeks passed and John kept trying to visit Sherlock, but he goes less frequently, as Mrs. Hudson continues to refuse him entry to see Sherlock. 'What is the point?' he thought.

All John wanted was answers. It wasn't that hard to comprehend. Or was it? John wanted to talk to Sherlock again, like the old days, but Sherlock has locked himself away.

Could Sherlock becoming a criminal? Or even committing some acts of corruption? Was Sherlock being duplicitous and still helping Moriarty? No one knows what is going on Sherlock's head. No one does. No one ever will. Sherlock Holmes is a mystery beyond our greatest minds. Sherlock is in self-proclaimed isolation.

What could John do now?

 _Authors Note:_

 _NO MOLLY! WHY DID YOU HAVE TO DIE? Oh wait, I killed her.. Sorry! Do not hate me, I am really nice, honestly!_

 _Disclaimer: I will never own Sherlock._

 _Only 4 more chapter left!_

 _What is going on with Sherlock? What is happening to Molly? Are these your questions? I bet they are! :) They will be answered soon. I really want to tell you! But I will not! Mwwaahhaa!_

 _If you can spot it, there is a way to recognise who dies! Can you see it? ;)_

 _I may be able to update in the week, if not the weekend. Then its the summer holidays! I will finish this story in the summer holidays! I don't want it to end, its to fun to write!_

 _Thank you for all the reviews. They mean so much to me. I would love to hear your reactions to Molly's death and what frightened her to death. Literally!_

 _That button down there, you know the review button? It is very lonely and depressed. It would really love to hear what you have to say. :D_

 _Until the next chapter…_

 _-TwilightMortal_

 _xxx_


	7. Chapter 7: The Milestone At The Window

**The Troublesome Tales of Sherlock and Moriarty**

Chapter 7: The Milestone At The Window

 _Previously on The Troublesome Tales: Could Sherlock becoming a criminal? Or even committing some acts of corruption? Was Sherlock being duplicitous and still helping Moriarty? No one knows what is going on Sherlock's head. No one does. No one ever will. Sherlock Holmes is a mystery beyond our greatest minds. Sherlock is in self-proclaimed isolation. What could John do now?_

Chapter 7:

The following Sunday, that turned out to be quite sunny and bright, the opposite to what was lurking in the depths of the dark and dreary London's underground tunnels and subway. Where the fearsome Moriarty could be waiting to strike. Wrecking havoc, where ever he went.

However, John and Mycroft had just finished their weekly meal together at the same location as they always did. Their local fish and chip shop. They were walking, once more down Baker street, talking about work and general rumours. They would talk about anything to take their fatigued minds of Sherlock, they both knew he would not becoming out of his own isolation for duration of years that would upset them terribly.

"Sherlock is back into hiding?" Mycroft said, he sounded like he knew that Sherlock would go back into his own company, but Mycroft didn't want to admit it, not yet.

They stop outside a door. A door that they know well, to well. The black door that was holding weak paint, that was almost at the stage of ripping. It held proudly three numbers and a lower case letter,with a rusted once golden door knocker. It was almost had a double meaning; proud and sophisticated but old and rusty.

The same accursed door that lead to a very treasured friend of theirs that was locking himself away for no apparently sane reason. He was cutting of his connections to the outside world.

Usually, it was open for any customer to walk thought and give Sherlock a baffling case that would keep him occupied for a week but then he would solve the mystery. Now, it was bolted shut, with no signs of being re-opened. It held no promise that it would open again to the general public to give them support, knowing that their case would be solved quickly and efficiently.

~OooO~

"Should I knock on the door?" John asked, looking longingly at the door of 221B Baker Street.

He looked at Mycroft, he was biting his chapped lips, almost saying ' _do not bother_ '.

"Your right" John said sadly, ' _why waste time'_ John thought. He wanted to try and see Sherlock, but Mrs. Hudson would not let him enter, she wouldn't even let him get too close to the house, like it was a deadly disease that could kill him within seconds.

"Moriarty will never be seen again" Mycroft said, Mycroft seemed muddled. Overjoyed that they would to have to worry about Moriarty any more but bitter that he could not face justice that he so rightly deserved. "I'm glad he has gone."

"I agree, he is such a nutcase" John said immediately, then he smiled, he had called Moriarty a 'nutcase.'

Both men laughed for a few mere seconds before composing themselves again.

"You know I actually spoke to Hyde" John said, looking into the distance.

"What did you think of him?" Mycroft said, almost eager to hear John's description of the maverick.

"He was.." John paused, trying to recall the deformed features of the man that was Moriarty "When I met him, I was filled with a fierce feeling of revulsion."

"It is impossible to see Moriarty with out feeling under the weather" Mycroft remarked.

John laughed, humourlessly. Remembering what he felt like when he first met Moriarty. Shock. Horror. Disgust. Fear. Anxiety. Despair. Dread. Terror. Fright. To say the least, John was completely and absolutely petrified of Moriarty.

"I am very worried about Sherlock's health" John said, trying to change the subject quickly.

"Yes, his sudden changes of behaviour must be impacting his mental health quite a bit." Mycroft said, showing some concern for his younger brother.

"If, Mrs, Hudson let us in, then our company could strengthen him, make him want to be sociable again" John said, then he realised that his plan would not work. Even before all this mess, Sherlock was never _that_ sociable.

"John? Mycroft?" said a familiar voice, that made John and Mycroft jump in surprise. To anyone around them, they would have jumped a few small centimetres of the concrete pavement.

Both Mycroft and John swivelled around to find who owned that voice, they couldn't see the owner.

"I'm up here" the voice said.

Mycroft and John looked up to see Sherlock sitting by the window, looking like a lonely prisoner in his own proclaimed solitary confinement. Sherlock looked _very_ ill. From where Sherlock was sitting, enjoying the fresh air, John remembered how Sherlock looked before, he looked near death. Now, Sherlock looked even worse.

"Sherlock" John breathed, he was relieved to see Sherlock in a semi-healthy way, even though he didn't know that he would ever see Sherlock again.

"How are you?" John asked, once he had collected his thoughts from the surroundings.

"I feel very low" Sherlock complained, brushing some specks of dust that seemed to be sheltered on his comfortable plush dark red blanket.

"Maybe if you actually go outside, then you may feel a little bit better." John suggested.

"I..I cannot join you. I'm sorry John" Sherlock said, looking quite apologetic "But thank you for the kind offer."

"Ok" John said.

"I would love to invite you for a longer chat" Sherlock paused "The flat is not.. really tidy."

John remembered that the flat that they both used to share, was never tidy. Why was he now bothered?

"Why cannot we just chat from where we are?" John suggested.

Sherlock smiled. It was a genuine smile, that John had never seen before. It brought a smile to John's melancholy face.

Out of the blue, Sherlock's featured changed. Sherlock froze in an expression of hopeless terror and despair. His expression was swift and so despicable.

John and Mycroft were stunned, their blood froze. They had to stop their jaws from dropping from the confusion.

Sherlock dropped the ground. Then a hand rose and slammed the window viciously.

Without a word, John and Mycroft looked around, searching for witnesses. They didn't want rumours in the media spreading that 'Sherlock was finally going mad'. Mycroft did not want his brother's 'business' to tampered Being, satisfied that no one had seen what had happened to Sherlock.

As they walked quickly down the street, they did not speak. They were too shocked from the scene at Sherlock's flat.

"What happened?" John said, finally breaking the awkward silence that was making John nervous.

"I have no clue" Mycroft said honestly. John couldn't believe this. The man that knew everything, possibly in the world, had no clue about his own younger brother. John couldn't believe his ears.

"What is happening to Sherlock?" Both men said at the same time, trying to make sense of what they had just witnessed.

Sherlock, writhing in pain and agony. Who hid from them, when instead, Sherlock could have called for help but he hid out the way, out of sight. Out the way of getting help.

This was an event that changed everything. They wanted to believe that Sherlock was okay. Inside, they both did not want to believe that Sherlock was going to be fine. They knew they were lying to themselves. They couldn't bear to believe what was staring them right in the face.

Something had happened to Sherlock. They couldn't help him. They didn't know what. But, did they want to?

~OooO~

John walked up the path to his house. He unlocked the door, walked through, then slammed the door with frustration.

"John?" Mary said, walking in the direction of the front door.

"Mary." John said, happy to see her comforting smile.

"What is wrong?" Mary said, her smile morphing into a frown.

"Sherlock. He was sitting by the window, looking longingly outside. After a short conversation, he suddenly was overcome with pain. He ducked down, out of sight, then closed the window" John said, realising that Sherlock could have had a stroke or even dying, but why did he not call for help?

"That is definitely odd. But, John, Sherlock has been acting strange lately. This abnormal behaviour must be expected." Mary suggested.

"Your right." John said, sighing "I should have suspected this."

He walked over to his comfy arm chair, he almost fell into the chair. It was similar to his old chair back at Sherlock's unkempt flat.

'Yikes, that feels like a lifetime ago. Where did everything go?' John thought, trying to recall past memories, but they were hazy and cloudy.

John could barely remember the flat. He hasn't been there for a couple of months. It was coming up to a year, John wanted to find a magic lamp and talk to a genie, he would ask for everything to go back to normal.

He would erase the Moriarty nonsense and try to eradicate the source, he would kill Moriarty. He would watch the life leave Moriarty and thrive in the knowledge that he would never again harm his best friend; Sherlock Holmes.

Although, if he used his wish to jump forwards in time, to when Moriarty had died, his friendship with Sherlock would have grown stronger, since they would have been through a rough ordeal. That would have change them forever.

To get to the best parts of life, you have to go the abominable times. John felt as if his life was clouded with atrocious times, that was bringing, his once bubbly soul, down.

Life was unsatisfactory for John. It was unacceptable. Everything needed to change. Everything led back to James Moriarty, John's fantasy world where he met a genie and change the timeline of events. Some events, were valuable, like when he, Molly and Sherlock were analysing the woman's death. That was John's most recent favourite memory. He treasured this as it was his lifeline, as if he forgot it, then he would die a painful excruciating death.

John would remember it for years to come. As it was his last memory with a semi-normal Sherlock and an existing Molly. This would get him through the darkness that was creeping up on him. And it was haunting him. It was ready to strike. And it will strike with considerate force.

 _Authors Note:_

 _This is a key chapter. This is the last chapter that is low key and isn't fast paced. Hold on, its a rocky ride from here on out._

 _I am really looking forwards to the next chapter.. It was my favourite chapter apart from the last one. So much happened. SOME ONE MAJOR DIES! YOU WILL NEVER SEE IT COMING! Lets just say that you will be screaming at me for answers, which you will get in the next chapter. (chapter 9) I feel mean for torturing you. Mwwaahhaa! Anyone want to guess who dies? :)_

 _What is happening to Sherlock? Anyone want to hazard a guess?_

 _Disclaimer: I do not own Sherlock, if I did, then I would force the actors to do season 4 right now. Anyone want to join me? :) Dreams…._

 _This chapter was originally 598 words, so this took me ages…. I really wanted to skip this and change it completely, but it would effect the plot of the story._

 _Thank you for the reviews. I really appreciate them. That review button, right down there, needs you to remind him that he is not alone. He needs friends! He needs you! Lol! ;)_

 _I may be able to update in two days. This chapter took me about two nights. I hope that you can wait until about Thursday. If you are lucky, then I will update Tomorrow!_

 _Any questions, just PM me._

 _Until the next chapter!_

 _-TwilightMortal_

 _xxx_


	8. Chapter 8: The Last Day

**The Troublesome Tales of Sherlock and Moriarty**

Chapter 8: The Last Day

 _Previously on The Troublesome Tales: John's fantasy world where he met a genie and change the timeline of events. Some events, were valuable, like when he, Molly and Sherlock were analysing the woman's death. That was John's most recent favourite memory. He treasured this as it was his lifeline, as if he forgot it, then he would die a painful excruciating death. John would remember it for years to come. As it was his last memory with a semi-normal Sherlock and an existing Molly. This would get him through the darkness that was creeping up on him. And it was haunting him. It was ready to strike. And it will strike with considerate force._

Chapter 8:

That night, John was watching the local London news, paying plenty of attention to what was happening in his city, despite feeling heartbroken that he couldn't help Sherlock while his friend was writhing in agony. He couldn't believe what he had seen, it didn't seem real. Turning his attention back to the television screen, he quickly got absorbed once again.

 _Knock, knock, knock._ The sound of someone knocking on his door, made John jump, he was not expecting anyone to knock on his door this late at night. He reluctantly switched off the television.

The knocks on the door brought John back to the real world, he was completely absorbed in the news. It was insanely fascinating to John. Anything that took his mind of Sherlock and Moriarty, he would try it. He wants some escapism and some difference. Recently, John's world has been completely involved in this mystery. Every second of every day, was about the mystery. John needed to take his mind of it, even if it was just for a few measly minutes a day.

Someone was at the door. John lazily got up from his comfy chair, walked over to the door and opened the blue wooden door to find Mrs Hudson, who was shivering on his door step. She was wearing a dark blue coat with a red scarf and purple knitted gloves.

"What are you doing here?" John asked almost dragging her inside, he was concerned about Mrs Hudson being out late at night in the cold.

"John. I feel that there has been some 'foul play' regarding Sherlock" she said anxiously, she was looking down to the floor, she was clearly distressed.

"What has happened?" John asked.

"I cannot really explain it. You must trust me, you need to see it for yourself."

John followed Mrs Hudson back into the dead of the cold night.

The night was dark and windy. It gave John the presence of a ghost watching them move through the murky and shadowy streets.

It was a wild, cold, seasonable night, with a pale moon, lying on her back as though the bitter wind had tilted the weak moon. The wind made talking to Mrs Hudson difficult, the wind almost took his shaky breath away. It seemed to have swept the streets unusually peeled of passengers, besides Mrs Hudson and John, thought he had never seen that part of London very.. deserted.

The street, when they got there, was all full of wind and dust, and the thin trees in the garden were lashing themselves along the fences.

The random litter fly effortlessly in the wind, waiting to attack someone by flying into their unsuspecting face. The feeling gave John more of a reason to walk quicker, as it gave him a feeling of impending disaster.

~OooO~

When they reached Sherlock's house, Mrs Hudson rushed up to the door, unlocked it with shivering fingers, she almost dropped the keys several times. Then she brought John up the stairs, towards the flat, which Sherlock currently owned.

"Hello, Sherlock?" she said, she put her small ears to the door, trying to talk to Sherlock through the closed door. "John is here to see you" she thought that the little mention of John, would make Sherlock open the door.

A gruff voice that John could barely hear properly responded. John could make out that he was saying something on the lines of _'I can receive no visitors.'_

Mrs Hudson pulled herself away from the door, then pulled John to the stairs.

"That clearly wasn't Sherlock." she insisted "It wasn't his voice".

John wondered if the unknown person had killed Sherlock, but why would he remain in the flat. Why not flee? Did they want to be captured? Did he want to be locked away in a lonely prison cell? Did he want to be charged with murder?

"The mysterious voice, always sent me out to some drugstore in London. It was ingredients that were in none of the stores that I went to. I had never even heard of the name." Mrs Hudson said.

"Does the mysterious man still have the list?" John asked hopefully.

"Yes he does. I keep seeing him in the flat. He comes out briefly to search for something, that I dare not think what. He looks nothing like Sherlock." she said, she seemed scared of the mystery man.

"Maybe Sherlock has some kind of disease that alters his voice and his features. Making him unrecognisable?" John suggested, Sherlock did see quite ill recently.

"No" she insisted "The man was smaller than Sherlock, he looked… just like Moriarty" she said staring up at John, shock and horror were present upon her wrinkled skin.

~OooO~

Once he heard the name; Moriarty. John's mind began to turn. He needed to search that damned flat. He turned around, looking for something sharp. Something that could break down a door. Where would it be? John remembered that he had a knife in his coat pocket.

"Can I please come inside" John demanded.

"John, for god's sake have mercy!" a voice yelled back "Leave me alone!"

John remembered that voice. His world was crashing down. He hated the person who owned that voice. It was Moriarty.

John pulled out his pocket-knife and jammed it into the door.

When they were able to go through the door, they quickly scanned the flat. Not too long after entering, Mrs Hudson had found something rather interesting.

"John." Mrs Hudson cried weakly, she was pointing to something that was on the floor.

John followed Mrs Hudson's gaze, what he saw astounded him greatly.

It was Moriarty. He was lying on the floor, with a crushed vial in his small hand. He had poisoned himself. Rather than let John hand him into the Police, Moriarty had poisoned himself. 'Coward' John thought.

"John, look." Mrs Hudson said "Look closer."

John looked closer at Moriarty. All he saw was a criminal, that didn't care who lived or who died. John knew that Moriarty had something to do with Lestrade's murder.

"I only see a criminal" John said truthfully.

"No John, what is he wearing?" Mrs Hudson insisted.

Once again, John glanced at the criminals body, he was wearing Sherlock's clothes. The thief. Although they were too enormous for Moriarty. It was like he was an ant in a shoe-box.

'Why was he wearing Sherlock's clothes?' John asked himself 'Why is he in Sherlock's house?'

When the real question was 'Why had he killed himself?'

~OooO~

Mrs Hudson and John thoroughly search the entire messy flat. There was no trace of Sherlock or even his corpse. Everything seemed like nothing had been changed. Nothing was different apart from Moriarty's corpse lying dead on the floor.

As well as the corpse, there was only an A5 piece of line paper attached to a mirror. Was Sherlock finally forgetting something important?

"It is strange to find Sherlock writing a note to himself" John said, trying to make sense of the letter "Doesn't he remember everything? What about his bloody mind palace? He can remember every fact under the sun, but he has to remind himself to go to sleep at night?"

John put the letter down, then found a letter on the table that was in front of the brown leather sofa. It was a large envelope, it contained three other envelopes. One was Sherlock's will, but instead of Moriarty's name being on the will, it was replaced by John's name. The second letter was addressed to John, it had todays date on it.

"Why don't you read it?" Mrs Hudson asked curiously.

Her question made John eager to open it. It was a clear indication that Sherlock was indeed alive. It brought a little bit more happiness to John's depressed heart.

The letter read:

' _John_ , — When this shall be in your hands, I shall have disappeared, under what circumstances I have not the power to foresee the future, but my instinct and all the circumstances of my anonymous situation tell me that the end is sure and must be early. Go and first read the letter which Molly warned me he was to give to you, and if you care to hear more, turn to the third letter, my full confession, only read it after Molly's letter.

Your unworthy and unhappy friend,

-SH'

"Mrs Hudson, I will return in the morning." John said, before he dashed of to his house. John felt as if he was Sherlock, when he had deduced a new clue that would lead him towards the answer that would break the mystery.

John wanted to know what was in Molly's letter and then he would read Sherlock's letter. John walked home quite briskly, he would stay awake all night if he needed to. He would know what had been going on. He felt quite relieved to know that the answer to his prayers was in these letters. One was in his hand and the other was waiting him at home at the top of a pile of mundane bills.

This mystery was about to come to an end and unravel. It was obviously well past the time for answers.

 _Authors Note:_

 _Did you see the big twist coming? I bet you didn't!_

 _Next chapter, I will explain the biggest question, that you might have._

 _It is basically John reading Molly's letter, so it will be based before Molly died and got ill. The reveal of some surprising news will leave you with more questions!_

 _Then in the final chapter, everything will be Sherlock's fuln account of what was going on in the whole story. So this is basically the last chapter. The last two are just other people's side of the story._

 _If once I have explained everything, then you have lingering questions, feel free to put them in a review or just PM me._

 _Disclaimer: I will never own Sherlock._

 _The original was around 4,000 words, so I hope I done this chapter justice. I could never write a chapter that long._

 _I am not sure when I will update next, the last couple of night, I have been on the computer all night. I do not feel that I should. Expect an update around about Friday, Saturday or Sunday, If not then Monday! I do want to finish this as soon as I can. So I can write more stories or more one shots. Any ideas on what I could write? I am open to suggestion. :)_

 _Thank you for all the reviews. They mean the world to me. It keeps me writing. That review button is starting to feel appreciated now, he feels more loved. Please keep him happy, I hate to see him all sad and lonely. It is heartbreaking._

 _If you really cannot stand the long way, I could send you really special sneak peak, all you have to do is review. It is that simple and you may find it in your inbox. Sadly any guest reviewers cannot get this. I am so sorry, but I have no way of sending you a sneak peak. :(_

 _Soon, all will be revealed. Any last minute guesses? I'd love to hear them._

 _Until the next chapter,_

 _-TwilightMortal_

 _xxx_


	9. Chapter 9: Molly Hooper's Version

**The Troublesome Tales of Sherlock and Moriarty**

Chapter 9: Molly Hooper's Version

 _Previously on The Troublesome Tales: John wanted to know what was in Molly's letter and then he would read Sherlock's letter. John walked home quite briskly, he would stay awake all night if he needed to. He would know what had been going on. He felt quite relieved to know that the answer to his prayers was in these letters. One was in his hand and the other was waiting him at home at the top of a pile of mundane bills._ _This mystery was about to come to an end and unravel. It was obviously well past the time for answers._

Chapter 9:

John was eager to read the fascinating note that Molly had left for him to read. It should shed some light on John's concerns.

So, in his eagerness, he almost ran the whole way home. Once he got inside, he bounded over to pile of letters and scavenged his diligent way through the stack, until he had found was he as looking for; Molly's Letter.

He opened the envelope, throwing it over his shoulder, not caring where it landed, he opened the letter as he walked into a chair, bumping into furniture along the way. Cursing the 'wretched furniture', John finally sat down, he was happy to hold the answers in his shaking hands. Once he finished shaking, he began to read Molly's letter. It went something like this…

Molly's Point of View: (Set before Molly dies)

After helping Sherlock with the last case, which Molly and John helped him solve, Molly received a letter. In short, Sherlock wanted Molly to go to his house and with Mrs. Hudson break into his house and remove a specific drawer and all its contents, then bring it to her house, where a man who would collect these items at precisely midnight.

Molly deduced that it was written hastily and in a mood of desperation. The bizarre letter gave no clear explanation but Sherlock promised that after this favour, Sherlock would clear everything up. This promise urged Molly to do as Sherlock asked.

~OooO~

So, Molly went to Sherlock's house, where she found Mrs Hudson and a locksmith. Just as Sherlock said she would. After a few measly minutes of small talk with Mrs Hudson. The locksmith broke into the room.

Molly looked around the room. She could remember all the times that Sherlock had asked her to come over or when John threw a party of some kind. Memories came flooding back, with tears threatening to fall.

But one tear managed to escape. Molly wiped it away before Mrs Hudson could see.

Before any more painful memories flashed back to haunt her, she quickly found the drawer that Sherlock had told her to find. She grabbed it and left the flat. She hurried home to look in the drawer, wanting to know what was inside the mysterious drawer.

~OooO~

At home, Molly sat down on a chair. She slowly peeled back the lid and peered inside the drawer.

All that was in the drawer was several vials containing what Molly thought was salt and a peculiar red liquid. There was also a notebook with many scribbles which dated back to be many years of experiments, with notations of _'TOTAL FAILURE'_ or _'DOUBLE'_. They were spread out over a long list of dates, but there were no helpful hints on what the experiment was.

~OooO~

When midnight was nearing, Molly waited patiently for her visitor. Could Sherlock be lying? she wondered 'or was he completely insane?'.

She sat in her living room, sitting on her sofa, tapping a melody to occupy herself as she waited.

~OooO~

As promised, at the precise stroke of midnight, there was a knock at the door.

Molly got up, anxious to know who was at her door.

She opened the door to see a small, evil-looking man, who was dressed in clothes much too large for him. It was, of course, Moriarty, but Molly had never seen Moriarty before, so she did not recognise him.

The man seemed nervous yet strangely excited. Molly couldn't understand why.

"Hello, my name is Molly. I guess you are hear for the contents of the drawer." she said

"Where is it?" he said, pushing Molly out of the way, his dark green eyes scanning the room viciously

"Errr… It is here" Molly said timidly, she was frightened of the man. To Molly, he seemed like he was the type of guy to hurt someone just because they were in his way. At this moment, she was completely correct. Molly showed the man into her living room, where the drawer was laying.

When the man saw the drawer, his eyes lit up like a child seeing his pile of presents on christmas morning.

He moved swiftly over to the drawer, he opened it grabbing out the contents and laying them on Molly's kitchen table.

"Can I have a glass please Molly?" he asked

"Sure.." Molly said, she went into her kitchen and pulled out a glass for the man. She then carefully walked over to the man who looked like he was about to burst.

She handed him the glass, which he poured the in the ingredients. He mixed them in the glass, the liquid turned from a purple colour to a light green colour.

The liquid changed colours in a record-breaking time of twenty seconds of mixing two opposite colours together. The change of colours made Molly disbelieving.

The man picked up the glass, he was about to drink the green liquid but paused

"Do you want me to leave and take this. Or should I stay and drink this here?" he asked kindly, but he did not seem like a man like him could be capable of being this kind. "Do you want to witness something that would change Science completely?"

"I have already seen this much." she declared "I have been involved in this quite deeply, I might as well see this to the end."

"Fine. Your skepticism of transcendental medicine will now be disproved" he said, he seemed to have known Molly. Molly had never seen this man before, but he knew that she disapproved transcendental medicine.

He inhaled slowly then put the glass to his chapped lips and gulped down the strange potion in one big monstrous gulp.

He cried out in pain, it sound felt as if the windows would smash, Molly felt as if her ear drums would break.

He reeled, staggered and clutched the table with a force that she thought would make a dent in the table or worse, break it in two halves.

He started at me with injected eyes. He gasped out in sheer pain. His face began to inflate and turn into a dark black colour.

His gruesome features began to melt and alter. His whole body swelled, it was changing, changing into a absolutely different matter all together. The prospect of a man's features, that would never alter, change was a huge shock to Molly.

The way his body changed, it made Molly feel under the weather. It was like she was in Summer but then Winter pushed Summer out of the way, without slowly changing the weather.

Molly sprang to her feet, she pulled herself to the wall papered wall, with a force that she did not know that she had built inside her. She shielded her face with her weak arms, her mind racing with terror. 'What on earth is happening?' she thought.

Nothing made sense anymore.

Nothing would be the same for Molly.

Her whole percept of the world had changed dramatically, within a few short seconds of time.

Once all the agonising screaming was over, Molly slowly peeled open her scared eyes, to see a man; pale, shaken and half-feinted. He looked like he was recently returned from the dead.

There, stood in front of her was not Moriarty. He was nowhere to be seen.

There stood Sherlock Holmes, the man that everyone believed was the hero, but he himself didn't believe in heroes. The man she loved, was a murderer. He had killed Lestrade. Her love for Sherlock had vanished entirely. It was a concept that Molly couldn't make herself find again.

Moriarty was Sherlock. Sherlock was Moriarty.

They were the same person.

Moriarty was Sherlock's evil alter ego.

~OooO~

 _'_ _What he told me in the next hour, I cannot bring my mind to set on paper._

 _I saw what I saw._

 _I heard what I heard._

 _My soul was sickened at it and yet now when that sight has faded from my eyes, I ask myself if I believe it, and I cannot answer._

 _My life has been shaken to its core. Sleep has completely left me, I cannot get any sleep, fear invades me. The mortal terror haunts by me at all hours of the duplicitous bright day and truthful dark night._

 _I feel that my days are now numbered, it hasn't been changed in my favour and if I must have to die, and yet I shall and will die questioning Sherlock still after he told me the truth._

 _When you find out, I hope for your sake, you will be able to help Sherlock find himself. He has thoroughly lost himself. In both senses of the words. My last request for you is to help him. Help him find the light, make him see the brighter and more desirable and lawful way of life._

 _As for the moral evil that_ _man_ _showed to me, even with tears of shame, I cannot, even in memory, live on it without a beginning of horror. If I live on, I will be clearly changed, everything I knew has been altered, in a way I never thought possible._

 _I will say but one thing, John, and that, if you can bring your mind to credit it, will be more than enough._

 _The monster who crept into my house that night was, on Sherlock's own revelation, known by the name of Moriarty and hunted for in every corner of London as the murderer of Lestrade. Mr. James Moriarty, or better known as Sherlock Holmes; the evil proportion'_

-Molly Hooper

 _Authors Note:_

 _Did you guess that Sherlock was Moriarty? I bet you will be screaming at the screen. Predominately, me…_

 _Look back at all the previous chapter, I have left obvious clues, that if you knew, then you would see them! I am sort of glad that no one picked up on them._

 _So now you know why Molly died and how she died. She died from pure terror and shock._

 _Next chapter is the last chapter! *cries* It will all be from Sherlock's point of view. It is his story of his life. Before I start the chapter, I am sorry if I get anything wrong._

 _Any question, feel free to ask. I will reply, because the secret I was holding back was just revealed.._

 _Remember, a few chapters back, I said there was a way to see who dies and in which chapter.. The answer is:_ _the name that is mentioned in the chapter title, is the character that dies_ _.._ _So Lestrade, Sherlock, Moriarty and Molly has died. I promise that no one else will die._ ** _I swear on my fan-fiction lifeline._**

 _Disclaimer: I will never own Sherlock, no matter how much I cry that Sherlock will not be released until 2017! :(_

 _The next chapter shall be up soon. Hopefully on Sunday, or if you all threaten me, then I will update on Saturday!_

 _Thank you for the lovely reviews! They make my day happier than it was already. Seriously getting two reviews in two minutes made me smile from ear to ear. Thanks to:_ _SlightlyStrangeGirl_ _,_ _Sherlock2201_ _,_ _Fairy friend 232,_ _Bananapants, Charlie2001,_ _Watch ine_ _and_ _Apple pearl 2309._

 _PLEASE DO NOT HATE ME but.. by the way, if you were wondering, in chapter eight, I basically killed Sherlock…_

 _Until the next chapter.. (Unless I die from you crazy fans! :P)_

 _-TwilightMortal_

 _xxx_


	10. Chapter 10: Sherlock's Full Statement

**The Troublesome Tales of Sherlock and Moriarty**

Chapter 10: Sherlock's Full Statement Of The Saga

 _Previously on The Troublesome Tales: As for the moral evil that man showed to me, even with tears of shame, I cannot, even in memory, live on it without a beginning of horror. If I live on, I will be clearly changed, everything I knew has been altered, in a way I never thought possible. I will say but one thing, John, and that, if you can bring your mind to credit it, will be more than enough. The monster who crept into my house that night was, on Sherlock's own revelation, known by the name of Moriarty and hunted for in every corner of London as the murderer of Lestrade. Mr. James Moriarty, or better known as Sherlock Holmes; the evil proportion…_

Chapter 10:

Sherlock had decent childhood. He had a brother and parents who loved him dearly. He was cared for, so he thrived. He had a large inheritance that in the future he could rely on, he had good health and a hardworking, semi-decent nature. All seemed well.

~OooO~

Sherlock's ability to be duplicitous allowed him to have a high standing reputation in London as 'the famous consulting detective, who could solve any case, no matter how tricky.' He could hide his wicked, devilish and cruel side easily. No one would be able to figure out that it was him committing unlawful acts of crime.

Sherlock had found himself leading a double life. He could be a respected detective then become an evil sociopathic murderer. Although, his preferred good natured side, kept feeling guilty about what he had committed.

When Sherlock started using his scientific knowledge to help him figure out the cause of death, it led him to transcendental studies. Which could help him divide the nature of man. Sherlock wanted to find a solution his own split nature.

Sherlock always told himself while experimenting, that 'Man is not truly one, but truly two.' He wanted to separate his good and evil natures.

~OooO~

After more research, Sherlock found a long awaited chemical solution that could aid him with separating himself into two equal sections. All his painful efforts had succeeded. He was beyond happy to have the potion that could split him into two.

He brought a large quantity of salt to go with a purple liquid, that he had concocted. After mixing the strange coloured solution, it was ready. The first batch was ready to drink. Sherlock was ready to transform.

Sherlock knew that he was risking his life, but he knew if this worked then it was a huge discovery. It would be the biggest discovery of the century.

Without another thought, he drank the potion. At first, he felt pain and sickness.

When the pain and sickness vanished. Sherlock felt strong and filled with a huge sensation to be reckless.

His body became smaller, it was shrinking. A bigger sensation of pain came over him.

When all the pain faded away, he felt different. He was smaller, it was down to that Sherlock had oppressed his darker nature. The whole new exterior represented his evil nature.

Sherlock looked in the mirror. Looking at himself after the torturous transformation. He was not repulsed by his new form, but he felt more alive, as James Moriarty was much younger than Sherlock.

~OooO~

Sherlock was delighted to be Moriarty. His first act of an immoral impulses were to trample an innocent teenager who was walking happily with her boyfriend, then he had blown up approximately three houses or more with innocent families inside. Moriarty didn't feel guilty that he had mercilessly killed parents and children, not one single bit of caring was shed to the deaths, that he had orchestrated.

Sherlock was a little bit too old to blow up buildings and escape how Moriarty escaped the ' _foolish_ ' London Yard's police force. Moriarty was younger and more able to move quicker.

Transforming himself into Moriarty gave Sherlock the easy exit for any anger, that he held in the day. It was his freedom from being a lawful detective, that always helped people. Sherlock had became bored of being the ' _good_ _guy_ ', he wanted to be the villain, that was in fairy tales.

~OooO~

After a few weeks of transforming into Moriarty, Sherlock knew that if people saw Moriarty diving into Sherlock's flat, they would suspect that he was helping him. So, Sherlock gave Moriarty a house, he also appointed a house keeper who he swore into secrecy.

Sherlock also set up a bank account for his alter ego, Sherlock knew that Mycroft and John would see that Sherlock was helping Moriarty.

Every time that Moriarty turned back into Sherlock, he felt no remorse for Moriarty's evil deeds, although Sherlock tried to change whatever he could without being noticed.

~OooO~

Two months before Lestrade's murder that Sherlock found something to worry about.

He has awoken to be Moriarty. In the night, he had involuntarily transformed into Moriarty! It was not with the help of the potion, Sherlock feared that Moriarty was becoming independent from the potion, so Sherlock locked himself away, just incase Moriarty appeared when Sherlock was out in public.

The incident convinced Sherlock that he must cease the transformation, or he would risk himself being forever being trapped as Moriarty.

~OooO~

Two months in, he caved into his desires to transform, once again he took the potion.

Moriarty, who had been repressed for so long, came out wild and unpredictable. He was vengefully savage, in this mood, he shot Lestrade to death, he delighted in the crime, smirking his usual way. He showed no remorse, on the other hand, before the transformation back into Sherlock, Sherlock regretted the crime. Sherlock was almost at tears, he had ruthfully murdered his friend.

The devastating nature of Lestrade's murder assured Sherlock never to transform again, as he feared Moriarty. Sherlock hated the other half of himself.

~OooO~

In the months after Lestrade's murder, John, Mycroft, Molly and Mrs Hudson had all noticed that a heavy weight had been lifted. They all though that everything was well with Sherlock, but Sherlock wasn't, he was far from being well.

Eventually, Sherlock became weary of innocence, so he complied with his darkest desires, not being Moriarty, but he had acted as Sherlock.

The sudden dive into darkness caused a spontaneous transformation into Moriarty, while Sherlock was walking through Hyde Park. Sherlock was sitting on a park bench, when he felt the transformation. He was far from the safety of his flat. Far from the potion.

Being Moriarty, he was immediately felt brave and more powerful. Sherlock knew that if he was found then the police would arrest him for the murder of Lestrade. He couldn't go to his flat without taking a great risk of being seen and captured.

He pulled up his coat and ran to the nearest hotel. He managed to secure a hotel room, which he sent a text to Molly telling her to go to his flat and get the potion for him.

Sherlock had shown Molly his transformation. He felt sorry for her, she had witnessed something completely mind blowing.

After that night, Sherlock had to take a double dose of the potion every six hours, to avoid Moriarty showing up unexpectedly, as the potion started to wear away, the dreaded transformation would begin. Sherlock had been struck with this when he had spoken to Mycroft and John out of the window. Which forced him to cease talking and hide, fearing that they would find out about his dual nature.

~OooO~

In Sherlock's last desperate hours, Moriarty was getting stronger, as Sherlock was getting weaker. It felt that Moriarty was feeding of Sherlock's energy, it was disappearing, quicker than Sherlock realised. Moriarty was becoming independent from Sherlock and the potion.

Sherlock hated Moriarty, he also knew that Moriarty hated him. They were almost strangers to one another. Even though, they were the other half of the other.

To add to Sherlock's panicky desperation, the salt which was needed for the potion was running out. He would not have enough for another potion. Besides, the liquid was also running low. For Sherlock, nothing was going right. He was all alone in the world. No one would be able to save him from himself. No one would believe that he was Moriarty. The public believed him to be their hero, solving case after case, putting away murderers and criminals that would do them harm.

Sherlock had saved people's lives. He had quickly deduced who would be attacked or even killed. Sherlock was a saviour. They wouldn't believe Sherlock if he announced that he was Moriarty. They would not believe that this was possible.

He had ordered Mrs Hudson to buy more salt, no store in London sold the right salt that he needed but he had quickly realised that the salt did not have the same effect. The previous dose of salt must have had an impurity to make the potion work. Sherlock was mad, he knew what would happen to him, he was angry with himself that he had allowed Moriarty to kill that many people.

If he had not created the potion in the first place, Moriarty would not have been existed. Sherlock was furious at himself for letting his get way out of hand.

~OooO~

Anticipating that the moment when Moriarty would take over Sherlock completely was coming nearer. He used the last of the potion to write a final letter to John.

 _'…_ _Now, that I write this letter to you, John. I do not know when faced with his huge discovery, that if Moriarty will commit suicide, if he doesn't then surely he will be arrested and spend the rest of his days rotting in a filthy prison cell._

 _The only thing that I do know is that, by now. Sherlock Holmes will be no more. Goodbye John.' -SH_

Sherlock put down his pen. Looking to his left, on the desk was a cup. He knew that he had to, he needed to put an end to Moriarty's evil reign of terror.

Sherlock Holmes **is** no more.

 _End_.

 _Authors Note:_

 _WOW. Was that a powerful ending or what?_

 _What a journey. Thank you to all my lovely readers. I send virtual cookies! You guys are amazing!_

 _So all the questions about Sherlock have now been answered. Such as; the window incident, Molly's death, why Sherlock was in hiding and so much more._

 _Just to clarify, the potion that killed Moriarty/Sherlock was Cyanide. That was the reference to the original books! It was what was used in the third chapter's murder victim. It was also what killed Jekyll/Hyde in the original story. Do read the original if you haven't already, it was incredible._

 _In this chapter, there was a reference to a character in the original story. Hyde park. (Moriarty is Hyde in this fanfic) Any more questions, ask me! I'd love to talk, I loved reading the original story._

 _There will be no sequel. I have no clue what to write, if I ever will. It will be in the far distance. I have no immediate desire to write a sequel anyway. If I did, I wouldn't know what to write!_

 _Thank you for all the support and reviews. They have given me the will to give up two hours my evenings and write these chapters. When I first decided to write this was back in September (2014)._

 _I never thought, that it would take me two months to write a story of this length! I honestly thought I would be writing this long into the summer holidays!_

 _Over these past two months, I have enjoyed writing this bizarre story, I had so much fun! I hope that you guys like this story, even if I did with hold what was actually going on.. I hope you now understand! :)_

 _Again, thank you a million!_

 _Until we meet again!_

 _-TwilightMortal_

 _xxx_


	11. Sequel: The Extraordinary Epilogue

**The Troublesome Tales of Sherlock and Moriarty**

Sequel One-shot: The Extraordinary Epilogue

 _Previously on The Troublesome Tales: Sherlock Holmes IS no more…_

John's Point of View:

John put down the letters with shaking hands.

His best friends was dead.

Molly and Sherlock were dead.

The person he hated the most, was his best friend's evil alter ego.

John was almost at tears at these new revelations. Tears were threatening to spill.

Surely, he wanted answers to the 'Moriarty Mystery' as he begun to call it. He would not have believed this was the actual answer to his countless prayers!

Sherlock had became an enigma. One that John didn't get answers to, until Sherlock had unexpectedly died. John knew he would start crying, but he wouldn't. He would be strong, he was the only person _alive_ that knew of Sherlock's new status.

No one would believe that Sherlock was dead. No one would believe that Sherlock had managed to create a potion that could split people's personality in half.

It would damage Sherlock's reputation, even though he was dead. It would damage his legacy. It would also be a ground-breaking scientific discovery!

Something told John that the knowledge of the potion needed to be kept an untold secret.

~OooO~

Over the next few weeks, Mary could see that there was a complete change in John's behaviour, she knew he was suffering with a problem that he was hiding.

So, one night, she confronted him.

Mary was furious due to John being miserable and depressed. His reaction to her outburst was matched with much more fury which ended with John giving Mary the letters from Molly and Sherlock.

When Mary had finished reading the letters, Mary and John had begun their everlasting grief for their friends, who they will never forget. That would be true, until they died.

~OooO~

While John worked at the clinic, he pondered whether he should give Mycroft the letters. It would give Mycroft a clear explanation of what actually happened to Sherlock.

So one night after a long day at work, John rushed home, picked up the letters and went to see Mycroft.

"Hello John" Mycroft said happily "What brings you here?"

"Hello, Mycroft" John paused "It..It is about.. Sh-Sh-Sh-Sherlock"

Mycroft invited John in to the Diogenes Club, where John handed Mycroft the letters.

"You might want to sit down" John offered

Mycroft sat down then started to read the letters.

At first he seemed to be amazed but as he continued to read the letter, his amazed facial expression turned to a frown.

When the realisation kicked in, that Sherlock, his younger brother was dead, Mycroft kept re-reading the letters, checking if there was any hope that Sherlock could have survived the battle between the two parts of himself.

John did not know if it was right thing to do was to tell Mycroft about Sherlock's fate. Mycroft had a right to know, after all he was Sherlock's older brother.

John didn't know what to say to Mycroft, so he left.

~OooO~

Without Sherlock, the world did not have a consulting detective to solve baffling mysteries.

Criminals went unpunished and unchecked. Scotland yard didn't solve many cases, when they did, it had taken them months to catch the criminal. They all knew that they needed Sherlock, but they didn't have a clue where he was or why he wasn't helping them.

John's life continued, nothing particularly interesting came into his life. Life for John was boring, life wasn't the same without Sherlock.

John kept trying to move on, he tried to make new friends, but they were not Sherlock. They would never compare to the famous consulting detective.

~OooO~

After Moriarty's body was discovered by the police, they had taken him to the local morgue. John had gone with them, inside John hoped that Molly was there, but one of Molly's colleagues had examined Moriarty's body. They had found nothing, nothing that could tie him to any of his 'killings'.

So, they had ordered him to be buried. Moriarty or as John knew him as 'Sherlock' was buried under a tall and old oak tree in a cemetery, with no one's grave nearby.

John kept visiting the grave, speaking to the stone, knowing that his best friend was buried there under another name. His alias. An alias that would never be uncovered to be Sherlock. Only John, Mary and Mycroft knew that Sherlock was there.

They were the only people who visited the grave. No one else knew that it was Sherlock under there.

Everyone always questioned them why they visited a supposed criminal's grave stone. Whenever some one asked, John, Mary or Mycroft never answered.

There was nothing to tell.

No one would understand.

No one would know why.

It was a secret that they would take to their graves.

~OooO~

Many decades had past.

John drew up his will.

So did Mary and Mycroft.

They all had something in common.

They all wanted to be buried in a specific location.

Everyone would question why they wanted to be buried there.

They had always wanted to be buried there.

Their wishes to be buried under a tall and old oak tree came true.

They would all be together again.

They would not be alone.

They were buried next 'Mr. James Moriarty.'

They all were buried next to Sherlock Holmes.

Death had come for them all.

 _'_ _Death is not the end of friendship,_

 _No one will ever be friendless._

 _We will meet again,_

 _We will not be in pain._

 _Together we will raise hell,_

 _This is not farewell.'_

 _Authors Note:_

 _See what a boring country walk inspires me to do… (don't ask!)_

 _Now, I can write no more, since all the main characters are dead. Sorry about that…_

 _A part of me wanted to know how John would react to Sherlock's death, but idea that cannot be spread over a full length story, hence this one-shot sequel. I hope I did not make you wait long for this and I hope that you were not disappointed of John's reaction._

 _I hope my poem is okay. I am not that good at writing poems…_

 _I promise, I have nothing left to write for this story! It is the end._

 _-TwilightMortal_

 _xxx_


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